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def main(argv):
parser = optparse.OptionParser()
parser.add_option("--output")
config, args = parser.parse_args(argv)
if not args:
pypeline.ui.print_err("%s takes at least one input file" % sys.argv[0])
sys.exit(1)
return call(input_files = args,
output_file = config.output)
def main(argv):
parser = optparse.OptionParser()
parser.add_option("-q", "--min-quality", type = int, default = 0)
parser.add_option("-F", "--exclude-flags", type = int, default = 0)
parser.add_option("--flag-as-sorted", default = False, action = "store_true")
config, args = parser.parse_args(argv)
if args:
pypeline.ui.print_err("%s does not take any arguments." % sys.argv[0])
sys.exit(1)
return call(min_quality = config.min_quality,
exclude_flags = config.exclude_flags,
flag_as_sorted = config.flag_as_sorted)
def main(argv):
parser = optparse.OptionParser()
parser.add_option("--jar-root", default = os.path.join(os.path.expanduser('~'), "install", "picard-tools"),
help = "Folder containing Picard JARs (http://picard.sf.net)")
options, args = parser.parse_args(argv)
if len(args) != 2:
ui.print_err("Usage: bam_pipeline move SRC DST")
ui.print_err(" where: SRC and DST are paths in the form TARGET/reads/SAMPLE/LIBRARY/LANE")
ui.print_err("Note that the second folder of the path (here \"reads/\") is ignored.")
return 1
source = parse_args(args[0])
destination = parse_args(args[1])
move_reads(source, destination)
move_bams(source, destination)
retag_bams(options, source, destination)
rm_files(source)
rm_files(destination)
print
return 0
def main(argv):
parser = optparse.OptionParser()
parser.add_option("--jar-root", default = os.path.join(os.path.expanduser('~'), "install", "picard-tools"),
help = "Folder containing Picard JARs (http://picard.sf.net)")
options, args = parser.parse_args(argv)
if len(args) != 2:
ui.print_err("Usage: bam_pipeline move SRC DST")
ui.print_err(" where: SRC and DST are paths in the form TARGET/reads/SAMPLE/LIBRARY/LANE")
ui.print_err("Note that the second folder of the path (here \"reads/\") is ignored.")
return 1
source = parse_args(args[0])
destination = parse_args(args[1])
move_reads(source, destination)
move_bams(source, destination)
retag_bams(options, source, destination)
rm_files(source)
rm_files(destination)
print
return 0
def main(argv):
parser = optparse.OptionParser()
parser.add_option("--jar-root", default = os.path.join(os.path.expanduser('~'), "install", "picard-tools"),
help = "Folder containing Picard JARs (http://picard.sf.net)")
options, args = parser.parse_args(argv)
if len(args) != 2:
ui.print_err("Usage: bam_pipeline move SRC DST")
ui.print_err(" where: SRC and DST are paths in the form TARGET/reads/SAMPLE/LIBRARY/LANE")
ui.print_err("Note that the second folder of the path (here \"reads/\") is ignored.")
return 1
source = parse_args(args[0])
destination = parse_args(args[1])
move_reads(source, destination)
move_bams(source, destination)
retag_bams(options, source, destination)
rm_files(source)
rm_files(destination)
print
return 0